Starting phenix.real_space_refine (version: dev) on Wed Apr 6 17:37:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/04_2022/7mxy_24076_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/04_2022/7mxy_24076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/04_2022/7mxy_24076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/04_2022/7mxy_24076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/04_2022/7mxy_24076_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxy_24076/04_2022/7mxy_24076_trim_updated.pdb" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.432 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 22": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 22265 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4457 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 4, 'TRANS': 278} Chain: "B" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4433 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 3, 'TRANS': 277} Chain: "C" Number of atoms: 4400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4400 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 3, 'TRANS': 275} Chain: "D" Number of atoms: 4446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4446 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 4, 'TRANS': 277} Chain: "E" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4422 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 4, 'TRANS': 276} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.99, per 1000 atoms: 0.49 Number of scatterers: 22265 At special positions: 0 Unit cell: (87.74, 99.51, 98.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 70 16.00 F 25 9.00 O 1911 8.00 N 1714 7.00 C 7416 6.00 H 11129 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 0 sheets defined 77.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.801A pdb=" N LYS A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 69 Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.916A pdb=" N ILE A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 99 Proline residue: A 91 - end of helix removed outlier: 5.167A pdb=" N PHE A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 4.167A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 147 Processing helix chain 'A' and resid 165 through 178 Processing helix chain 'A' and resid 182 through 205 Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.369A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 275 through 290 removed outlier: 5.481A pdb=" N GLU A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.605A pdb=" N LYS B 35 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 67 Processing helix chain 'B' and resid 71 through 77 removed outlier: 3.835A pdb=" N GLU B 75 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 100 Proline residue: B 91 - end of helix removed outlier: 5.064A pdb=" N PHE B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR B 100 " --> pdb=" O CYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 3.821A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 151 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.042A pdb=" N VAL B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 Processing helix chain 'B' and resid 250 through 270 removed outlier: 3.843A pdb=" N LYS B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 274 through 291 removed outlier: 5.487A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 removed outlier: 3.602A pdb=" N LYS C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 69 Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.820A pdb=" N ILE C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 100 Proline residue: C 91 - end of helix removed outlier: 5.233A pdb=" N PHE C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 removed outlier: 3.970A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 147 Processing helix chain 'C' and resid 149 through 152 No H-bonds generated for 'chain 'C' and resid 149 through 152' Processing helix chain 'C' and resid 165 through 178 Processing helix chain 'C' and resid 182 through 205 Processing helix chain 'C' and resid 209 through 225 removed outlier: 3.951A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 258 through 270 Processing helix chain 'C' and resid 274 through 288 removed outlier: 6.026A pdb=" N GLU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 removed outlier: 3.716A pdb=" N LYS D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA D 36 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N HIS D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 69 Processing helix chain 'D' and resid 71 through 77 removed outlier: 3.664A pdb=" N ILE D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 100 Proline residue: D 91 - end of helix removed outlier: 5.231A pdb=" N PHE D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N MET D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 removed outlier: 3.971A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 147 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 165 through 178 Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 209 through 225 removed outlier: 3.871A pdb=" N VAL D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 243 Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.721A pdb=" N TYR D 254 " --> pdb=" O VAL D 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 250 through 254' Processing helix chain 'D' and resid 258 through 270 Processing helix chain 'D' and resid 274 through 288 removed outlier: 5.953A pdb=" N GLU D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N HIS D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 37 removed outlier: 3.703A pdb=" N LYS E 35 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 68 Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.590A pdb=" N GLU E 75 " --> pdb=" O HIS E 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 99 Proline residue: E 91 - end of helix removed outlier: 5.020A pdb=" N PHE E 94 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 117 removed outlier: 4.114A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 152 removed outlier: 4.267A pdb=" N LEU E 151 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 Processing helix chain 'E' and resid 182 through 205 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.090A pdb=" N VAL E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 243 Processing helix chain 'E' and resid 250 through 255 Processing helix chain 'E' and resid 258 through 270 Processing helix chain 'E' and resid 274 through 288 removed outlier: 5.628A pdb=" N GLU E 283 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N HIS E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) 741 hydrogen bonds defined for protein. 2223 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.27 Time building geometry restraints manager: 22.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.00: 11089 1.00 - 1.20: 49 1.20 - 1.40: 4971 1.40 - 1.61: 6344 1.61 - 1.81: 100 Bond restraints: 22553 Sorted by residual: bond pdb=" SG CYS D 96 " pdb=" HG CYS D 96 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" SG CYS D 192 " pdb=" HG CYS D 192 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" ND2 ASN E 108 " pdb="HD21 ASN E 108 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" ND2 ASN E 108 " pdb="HD22 ASN E 108 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" ND2 ASN D 193 " pdb="HD21 ASN D 193 " ideal model delta sigma weight residual 0.860 0.977 -0.117 2.00e-02 2.50e+03 3.40e+01 ... (remaining 22548 not shown) Histogram of bond angle deviations from ideal: 95.96 - 103.18: 44 103.18 - 110.39: 21698 110.39 - 117.60: 7385 117.60 - 124.81: 10280 124.81 - 132.02: 1184 Bond angle restraints: 40591 Sorted by residual: angle pdb=" N ILE D 194 " pdb=" CA ILE D 194 " pdb=" C ILE D 194 " ideal model delta sigma weight residual 110.62 102.71 7.91 1.02e+00 9.61e-01 6.01e+01 angle pdb=" N LEU E 262 " pdb=" CA LEU E 262 " pdb=" C LEU E 262 " ideal model delta sigma weight residual 111.28 106.27 5.01 1.09e+00 8.42e-01 2.12e+01 angle pdb=" N THR D 109 " pdb=" CA THR D 109 " pdb=" CB THR D 109 " ideal model delta sigma weight residual 110.32 116.71 -6.39 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N GLY E 264 " pdb=" CA GLY E 264 " pdb=" C GLY E 264 " ideal model delta sigma weight residual 112.77 108.12 4.65 1.28e+00 6.10e-01 1.32e+01 angle pdb=" N PHE D 94 " pdb=" CA PHE D 94 " pdb=" C PHE D 94 " ideal model delta sigma weight residual 111.28 107.38 3.90 1.09e+00 8.42e-01 1.28e+01 ... (remaining 40586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7993 18.00 - 36.00: 846 36.00 - 54.00: 241 54.00 - 71.99: 50 71.99 - 89.99: 12 Dihedral angle restraints: 9142 sinusoidal: 3864 harmonic: 5278 Sorted by residual: dihedral pdb=" CA PHE C 90 " pdb=" C PHE C 90 " pdb=" N PRO C 91 " pdb=" CA PRO C 91 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA VAL C 158 " pdb=" C VAL C 158 " pdb=" N HIS C 159 " pdb=" CA HIS C 159 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA VAL E 213 " pdb=" C VAL E 213 " pdb=" N PHE E 214 " pdb=" CA PHE E 214 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 9139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1665 0.078 - 0.155: 81 0.155 - 0.233: 6 0.233 - 0.311: 3 0.311 - 0.388: 2 Chirality restraints: 1757 Sorted by residual: chirality pdb=" CA ASN D 193 " pdb=" N ASN D 193 " pdb=" C ASN D 193 " pdb=" CB ASN D 193 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA THR E 261 " pdb=" N THR E 261 " pdb=" C THR E 261 " pdb=" CB THR E 261 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA THR D 109 " pdb=" N THR D 109 " pdb=" C THR D 109 " pdb=" CB THR D 109 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1754 not shown) Planarity restraints: 3269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 108 " 0.192 2.00e-02 2.50e+03 1.92e-01 5.51e+02 pdb=" CG ASN E 108 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN E 108 " -0.180 2.00e-02 2.50e+03 pdb=" ND2 ASN E 108 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN E 108 " -0.272 2.00e-02 2.50e+03 pdb="HD22 ASN E 108 " 0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 193 " 0.180 2.00e-02 2.50e+03 1.79e-01 4.79e+02 pdb=" CG ASN D 193 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN D 193 " -0.169 2.00e-02 2.50e+03 pdb=" ND2 ASN D 193 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN D 193 " 0.261 2.00e-02 2.50e+03 pdb="HD22 ASN D 193 " -0.250 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 265 " -0.068 2.00e-02 2.50e+03 6.66e-02 6.65e+01 pdb=" CG ASN E 265 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN E 265 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN E 265 " -0.007 2.00e-02 2.50e+03 pdb="HD21 ASN E 265 " 0.094 2.00e-02 2.50e+03 pdb="HD22 ASN E 265 " -0.094 2.00e-02 2.50e+03 ... (remaining 3266 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1909 2.21 - 2.81: 47886 2.81 - 3.40: 67334 3.40 - 4.00: 90008 4.00 - 4.60: 137907 Nonbonded interactions: 345044 Sorted by model distance: nonbonded pdb=" O ASN B 257 " pdb=" HG1 THR B 261 " model vdw 1.611 1.850 nonbonded pdb=" O THR C 106 " pdb=" HG1 THR C 109 " model vdw 1.628 1.850 nonbonded pdb=" OE1 GLU C 229 " pdb="HD21 ASN C 234 " model vdw 1.634 1.850 nonbonded pdb=" OD1 ASN B 157 " pdb="HD22 ASN B 164 " model vdw 1.638 1.850 nonbonded pdb=" O CYS C 96 " pdb=" HG1 THR C 100 " model vdw 1.659 1.850 ... (remaining 345039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 289 or resid 1001)) selection = (chain 'B' and (resid 12 through 289 or resid 401)) selection = (chain 'C' and (resid 12 through 289 or resid 401)) selection = (chain 'D' and (resid 12 through 289 or resid 401)) selection = (chain 'E' and (resid 12 through 289 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 70 5.16 5 C 7416 2.51 5 N 1714 2.21 5 O 1911 1.98 5 F 25 1.80 5 H 11129 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.360 Extract box with map and model: 2.590 Check model and map are aligned: 0.370 Convert atoms to be neutral: 0.200 Process input model: 73.740 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.090 11424 Z= 0.397 Angle : 0.655 8.012 15507 Z= 0.369 Chirality : 0.042 0.388 1757 Planarity : 0.004 0.042 1886 Dihedral : 18.004 89.992 3862 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1396 helix: 1.49 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -1.73 (0.33), residues: 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 373 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 27 residues processed: 405 average time/residue: 1.0870 time to fit residues: 525.3652 Evaluate side-chains 380 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 353 time to evaluate : 1.594 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 4 average time/residue: 0.2650 time to fit residues: 3.7648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 0.0270 chunk 35 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 overall best weight: 2.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11424 Z= 0.205 Angle : 0.500 5.392 15507 Z= 0.279 Chirality : 0.036 0.155 1757 Planarity : 0.003 0.041 1886 Dihedral : 6.201 87.794 1555 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 5.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.23), residues: 1396 helix: 1.67 (0.16), residues: 1108 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 365 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 46 residues processed: 402 average time/residue: 1.0951 time to fit residues: 524.5970 Evaluate side-chains 397 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 351 time to evaluate : 1.609 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 30 residues processed: 16 average time/residue: 0.4971 time to fit residues: 13.3067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 11424 Z= 0.229 Angle : 0.502 4.957 15507 Z= 0.284 Chirality : 0.036 0.164 1757 Planarity : 0.003 0.040 1886 Dihedral : 5.999 89.270 1555 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 6.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.23), residues: 1396 helix: 1.69 (0.15), residues: 1110 sheet: None (None), residues: 0 loop : -1.71 (0.34), residues: 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 367 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 43 residues processed: 409 average time/residue: 1.1404 time to fit residues: 553.9504 Evaluate side-chains 398 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 355 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 27 residues processed: 17 average time/residue: 0.7587 time to fit residues: 18.5761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.2980 chunk 95 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN D 157 ASN D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 11424 Z= 0.274 Angle : 0.525 5.161 15507 Z= 0.298 Chirality : 0.038 0.169 1757 Planarity : 0.004 0.048 1886 Dihedral : 5.906 89.680 1555 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 6.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.22), residues: 1396 helix: 1.55 (0.15), residues: 1109 sheet: None (None), residues: 0 loop : -1.74 (0.34), residues: 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 357 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 51 residues processed: 400 average time/residue: 1.1119 time to fit residues: 529.9424 Evaluate side-chains 405 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 354 time to evaluate : 1.828 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 34 residues processed: 18 average time/residue: 0.6906 time to fit residues: 18.3739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN D 157 ASN D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.088 11424 Z= 0.443 Angle : 0.623 5.304 15507 Z= 0.358 Chirality : 0.042 0.175 1757 Planarity : 0.005 0.071 1886 Dihedral : 6.233 87.764 1555 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 6.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1396 helix: 0.98 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : -1.90 (0.33), residues: 295 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 364 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 56 residues processed: 411 average time/residue: 1.1035 time to fit residues: 541.7357 Evaluate side-chains 410 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 354 time to evaluate : 1.663 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 56 outliers final: 39 residues processed: 19 average time/residue: 0.7376 time to fit residues: 20.0483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 111 optimal weight: 0.0980 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11424 Z= 0.193 Angle : 0.497 6.264 15507 Z= 0.278 Chirality : 0.036 0.158 1757 Planarity : 0.003 0.068 1886 Dihedral : 5.755 83.021 1555 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 5.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.22), residues: 1396 helix: 1.58 (0.15), residues: 1108 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 368 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 44 residues processed: 411 average time/residue: 1.1380 time to fit residues: 558.2759 Evaluate side-chains 402 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 358 time to evaluate : 1.783 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 44 outliers final: 36 residues processed: 11 average time/residue: 0.6072 time to fit residues: 11.2073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 11424 Z= 0.385 Angle : 0.596 5.360 15507 Z= 0.340 Chirality : 0.041 0.171 1757 Planarity : 0.004 0.061 1886 Dihedral : 6.050 83.588 1555 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 6.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1396 helix: 1.16 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -1.80 (0.33), residues: 297 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 362 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 52 residues processed: 407 average time/residue: 1.1227 time to fit residues: 544.3514 Evaluate side-chains 407 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 355 time to evaluate : 1.797 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 52 outliers final: 38 residues processed: 17 average time/residue: 0.8366 time to fit residues: 20.1204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 11424 Z= 0.285 Angle : 0.555 6.083 15507 Z= 0.313 Chirality : 0.038 0.163 1757 Planarity : 0.004 0.044 1886 Dihedral : 5.924 84.342 1555 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 5.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.22), residues: 1396 helix: 1.29 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -1.79 (0.33), residues: 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 362 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 47 residues processed: 407 average time/residue: 1.0964 time to fit residues: 533.9291 Evaluate side-chains 404 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 357 time to evaluate : 1.691 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 47 outliers final: 37 residues processed: 12 average time/residue: 0.4955 time to fit residues: 10.5230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 11424 Z= 0.348 Angle : 0.585 5.899 15507 Z= 0.332 Chirality : 0.040 0.166 1757 Planarity : 0.004 0.053 1886 Dihedral : 6.054 85.647 1555 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 5.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1396 helix: 1.14 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -1.81 (0.33), residues: 297 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 357 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 46 residues processed: 398 average time/residue: 1.1605 time to fit residues: 554.6802 Evaluate side-chains 400 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 354 time to evaluate : 1.725 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 46 outliers final: 38 residues processed: 10 average time/residue: 0.4847 time to fit residues: 9.4393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS B 245 ASN D 252 GLN ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11424 Z= 0.172 Angle : 0.511 7.015 15507 Z= 0.280 Chirality : 0.036 0.154 1757 Planarity : 0.003 0.043 1886 Dihedral : 5.584 81.544 1555 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.23), residues: 1396 helix: 1.69 (0.16), residues: 1109 sheet: None (None), residues: 0 loop : -1.69 (0.34), residues: 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 374 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 37 residues processed: 411 average time/residue: 1.1406 time to fit residues: 557.0093 Evaluate side-chains 403 residues out of total 1156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 366 time to evaluate : 1.693 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 33 residues processed: 5 average time/residue: 0.3038 time to fit residues: 4.8099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN B 159 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.233043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.225854 restraints weight = 31344.941| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 0.86 r_work: 0.4625 rms_B_bonded: 0.84 restraints_weight: 0.5000 r_work: 0.4611 rms_B_bonded: 1.07 restraints_weight: 0.2500 r_work: 0.4590 rms_B_bonded: 1.49 restraints_weight: 0.1250 r_work: 0.4559 rms_B_bonded: 2.18 restraints_weight: 0.0625 r_work: 0.4514 rms_B_bonded: 3.29 restraints_weight: 0.0312 r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.085 11424 Z= 0.461 Angle : 0.650 6.871 15507 Z= 0.370 Chirality : 0.044 0.169 1757 Planarity : 0.005 0.071 1886 Dihedral : 6.133 85.825 1555 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 4.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1396 helix: 0.99 (0.15), residues: 1102 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 294 =============================================================================== Job complete usr+sys time: 8143.54 seconds wall clock time: 143 minutes 56.06 seconds (8636.06 seconds total)